# Tools for the Differential Analysis of Proteins Abundance with R

## Documentation for package ‘DAPAR’ version 1.26.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P Q R S T U V W

## -- A --

aggregateIter | xxxx
aggregateIterParallel | xxxx
aggregateMean | Compute the intensity of proteins as the mean of the intensities of their peptides.
AggregateMetacell | Symbolic product of matrices
aggregateSum | Compute the intensity of proteins with the sum of the intensities of their peptides.
aggregateTopn | Compute the intensity of proteins as the sum of the intensities of their n best peptides.
averageIntensities | Average protein/peptide abundances for each condition studied

## -- B --

barplotEnrichGO_HC | A barplot that shows the result of a GO enrichment, using the package 'highcharter'
barplotGroupGO_HC | A barplot which shows the result of a GO classification, using the package 'highcharter'
boxPlotD_HC | Builds a boxplot from a dataframe using the library 'highcharter'
BuildAdjacencyMatrix | Function matrix of appartenance group
BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by using the previous peptide dataset.
BuildColumnToProteinDataset_par | creates a column for the protein dataset after agregation by using the previous peptide dataset.
buildGraph | Display a CC
BuildMetaCell | xxxx

## -- C --

check.conditions | Check if the design is valid
check.design | Check if the design is valid
checkClusterability | Prepare the data for subsequent clustering
classic1wayAnova | Function to perform a One-way Anova statistical test on a MsnBase dataset
compareNormalizationD_HC | Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'highcharter'
compute_t_tests | xxxxxx
corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'exprs()' table.
CountPep | Compute the number of peptides used to aggregate proteins
createMSnset | Creates an object of class 'MSnSet' from text file
CVDistD_HC | Distribution of CV of entities

## -- D --

dapar_hc_chart | Customised resetZoomButton of highcharts plots
dapar_hc_ExportMenu | Customised contextual menu of highcharts plots
deleteLinesFromIndices | Delete the lines in the matrix of intensities and the metadata table given their indice.
densityPlotD_HC | Builds a densityplot from a dataframe
diffAnaComputeFDR | Computes the FDR corresponding to the p-values of the differential analysis using
diffAnaGetSignificant | Returns a MSnSet object with only proteins significant after differential analysis.
diffAnaSave | Returns a 'MSnSet' object with the results of the differential analysis performed with 'limma' package.
diffAnaVolcanoplot | Volcanoplot of the differential analysis
diffAnaVolcanoplot_rCharts | Volcanoplot of the differential analysis
display.CC.visNet | Display a CC

## -- E --

enrich_GO | Calculates GO enrichment classes for a given list of proteins/genes ID. It results an enrichResult instance.
ExtendPalette | Extends a base-palette of the package RColorBrewer to n colors.

## -- F --

finalizeAggregation | Finalizes the aggregation process
findMECBlock | Finds the LAPALA into a 'MSnSet' object
formatLimmaResult | xxxx
formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models summaries
fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic

## -- G --

get.pep.prot.cc | Build the list of connex composant of the adjacency matrix
GetCC | Returns the contains of the slot processing of an object of class 'MSnSet'
GetColorsForConditions | Builds a complete color palette for the conditions given in argument
GetDetailedNbPeptides | Computes the detailed number of peptides for each protein
GetDetailedNbPeptidesUsed | Computes the detailed number of peptides used for aggregating each protein
getIndicesConditions | Gets the conditions indices.
getIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix string
GetIndices_BasedOnConditions | Search lines which respects request on one or more conditions.
GetIndices_MetacellFiltering | Delete the lines in the matrix of intensities and the metadata table given their indice.
GetIndices_WholeLine | Search lines which respects query on all their elements.
GetIndices_WholeMatrix | Search lines which respects request on one or more conditions.
GetKeyId | xxxx
getListNbValuesInLines | Returns the possible number of values in lines in the data
GetMatAdj | Returns the contains of the slot processing of an object of class 'MSnSet'
GetMetacell | xxxx
GetNbPeptidesUsed | Computes the number of peptides used for aggregating each protein
getNumberOf | Number of lines with prefix
getNumberOfEmptyLines | Returns the number of empty lines in the data
getPourcentageOfMV | Percentage of missing values
getProcessingInfo | Returns the contains of the slot processing of an object of class 'MSnSet'
getProteinsStats | Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.
getQuantile4Imp | Quantile imputation value definition
getTextForAggregation | Build the text information for the Aggregation process
getTextForAnaDiff | Build the text information for the Aggregation process
getTextForFiltering | Build the text information for the filtering process
getTextForGOAnalysis | Build the text information for the Aggregation process
getTextForHypothesisTest | Build the text information for the hypothesis test process
getTextForNewDataset | Build the text information for a new dataset
getTextForNormalization | Build the text information for the Normalization process
getTextForpeptideImputation | Build the text information for the peptide Imputation process
getTextForproteinImputation | Build the text information for the protein Imputation process
GetTypeofData | xxxx
Get_AllComparisons | Returns list that contains a list of the statistical tests performed with DAPAR and recorded in an object of class 'MSnSet'.
GlobalQuantileAlignment | Normalisation GlobalQuantileAlignement
GOAnalysisSave | Returns an 'MSnSet' object with the results of the GO analysis performed with the functions 'enrichGO' and/or 'groupGO' of the 'clusterProfiler' package.
GraphPepProt | Function to create a histogram that shows the repartition of peptides w.r.t. the proteins
group_GO | Calculates the GO profile of a vector of genes/proteins at a given level of the Gene Ontology

## -- H --

hc_logFC_DensityPlot | Density plots of logFC values
hc_mvTypePlot2 | Distribution of Observed values with respect to intensity values
heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'
heatmapForMissingValues | This function is inspired from the function 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'. For more information, please refer to the help of the heatmap.2 function.
histPValue_HC | Plots a histogram ov p-values

## -- I --

impute.pa2 | Missing values imputation from a 'MSnSet' object
inner.aggregate.iter | xxxx
inner.aggregate.topn | xxxx
inner.mean | xxxx
inner.sum | xxxx

## -- L --

LH0 | xxxxxx
LH0.lm | xxxxxx
LH1 | xxxxxx
LH1.lm | xxxxxx
limmaCompleteTest | Computes a hierarchical differential analysis
listSheets | This function returns the list of the sheets names in a Excel file.
LOESS | Normalisation LOESS

## -- M --

make.contrast | Builds the contrast matrix
make.design | Builds the design matrix
make.design.1 | Builds the design matrix for designs of level 1
make.design.2 | Builds the design matrix for designs of level 2
make.design.3 | Builds the design matrix for designs of level 3
match.metacell | Similar to the function 'is.na' but focused on the equality with the paramter 'type'.
MeanCentering | Normalisation MeanCentering
metacell.def | Metadata vocabulary for entities
MetaCellFiltering | Filter lines in the matrix of intensities w.r.t. some criteria
MetacellFilteringScope | Lists the metacell scopes for filtering
metacellHisto_HC | Histogram of missing values
metacellPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per condition
metacellPerLinesHisto_HC | Bar plot of missing values per lines using highcharter
Metacell_generic | Sets the metacell dataframe
Metacell_maxquant | Sets the metacell dataframe
Metacell_proline | Sets the metacell dataframe
metacombine | Combine peptide metadata to build protein metadata
mvImage | Heatmap of missing values
my_hc_chart | Customised resetZoomButton of highcharts plots
my_hc_ExportMenu | Customised contextual menu of highcharts plots

## -- N --

nonzero | Retrieve the indices of non-zero elements in sparse matrices
normalizeMethods.dapar | List normalization methods with tracking option
NumericalFiltering | Removes lines in the dataset based on numerical conditions.
NumericalgetIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix string

## -- P --

pepa.test | PEptide based Protein differential Abundance test
plotJitter | Jitter plot of CC
plotJitter_rCharts | Display a a jitter plot for CC
plotPCA_Eigen | Plots the eigen values of PCA
plotPCA_Eigen_hc | Plots the eigen values of PCA with the highcharts library
plotPCA_Ind | Plots individuals of PCA
plotPCA_Var | Plots variables of PCA
postHocTest | Post-hoc tests for classic 1-way ANOVA
proportionConRev_HC | Barplot of proportion of contaminants and reverse

## -- Q --

QuantileCentering | Normalisation QuantileCentering

## -- R --

rbindMSnset | Similar to the function 'rbind' but applies on two subsets of the same 'MSnSet' object.
readExcel | This function reads a sheet of an Excel file and put the data into a data.frame.
reIntroduceMEC | Put back LAPALA into a 'MSnSet' object
removeLines | Removes lines in the dataset based on a prefix string.

## -- S --

samLRT | xxxxxx
saveParameters | Saves the parameters of a tool in the pipeline of Prostar
scatterplotEnrichGO_HC | A dotplot that shows the result of a GO enrichment, using the package 'highcharter'
search.metacell.tags | Search pattern in metacell vocabulary
SetCC | Returns the connected components
SetMatAdj | Record the adjacency matrices in a slot of the dataset of class 'MSnSet'
Set_POV_MEC_tags | Sets the MEC tag in the metacell
splitAdjacencyMat | splits an adjacency matrix into specific and shared
StringBasedFiltering | Removes lines in the dataset based on a prefix strings (contaminants, reverse or both).
StringBasedFiltering2 | Removes lines in the dataset based on a prefix strings.
SumByColumns | Normalisation SumByColumns
SymFilteringOperators | xxx

## -- T --

test.design | Check if xxxxxx
translatedRandomBeta | Generator of simulated values

## -- U --

univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb annotation package. Careful : org.Pf.plasmo.db : no ENTREZID but ORF
UpdateMetacell | Update metacell after imputation

## -- V --

violinPlotD | Builds a violinplot from a dataframe
visualizeClusters | Visualize the clusters according to pvalue thresholds
vsn | Normalisation vsn

## -- W --

wrapper.compareNormalizationD_HC | Builds a plot from a dataframe
wrapper.corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the 'exprs()' table
wrapper.CVDistD_HC | Distribution of CV of entities
wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm.
wrapper.heatmapD | This function is a wrapper to 'heatmap.2' that displays quantitative data in the 'exprs()' table of an object of class 'MSnSet'
wrapper.impute.detQuant | Wrapper of the function 'impute.detQuant' for objects of class 'MSnSet'
wrapper.impute.fixedValue | Missing values imputation from a 'MSnSet' object
wrapper.impute.KNN | KNN missing values imputation from a 'MSnSet' object
wrapper.impute.mle | Imputation of peptides having no values in a biological condition.
wrapper.impute.pa | Imputation of peptides having no values in a biological condition.
wrapper.impute.pa2 | Missing values imputation from a 'MSnSet' object
wrapper.impute.slsa | Imputation of peptides having no values in a biological condition.
wrapper.mvImage | Heatmap of missing values from a 'MSnSet' object
wrapper.normalizeD | Normalisation
wrapper.pca | Compute the PCA
wrapperCalibrationPlot | Performs a calibration plot on an 'MSnSet' object, calling the 'cp4p' package functions.
wrapperClassic1wayAnova | Wrapper for One-way Anova statistical test
wrapperRunClustering | Run a clustering pipeline of protein/peptide abundance profiles.
write.excel | This function exports a data.frame to a Excel file.
writeMSnsetToCSV | Exports a MSnset dataset into a zip archive containing three zipped CSV files.
writeMSnsetToExcel | This function exports a 'MSnSet' object to a Excel file.